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Crystal Structure Analysis of Space-grown Lysozyme
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5KXK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIQUID DIFFUSION 4.6 296 PEG 6000, NaCl, Na Acetate
Crystal Properties Matthews coefficient Solvent content 1.76 29.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.97 α = 90 b = 75.97 β = 90 c = 34.87 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M Flat Si Rh coated M0, Kirkpatrick-Baez flat bent Si M1 & M2 2019-04-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.97946 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.675 53.719 99.6 0.085 0.093 0.037 11.7 6.1 3147 3147
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.675 2.82 99.7 0.777 0.777 0.843 0.319 1 6.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5kxk 2.68 30 2952 169 99.17 0.2479 0.2441 0.253 0.3063 0.2875 RANDOM 73.562
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -1.63 -1.63 3.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.091 r_dihedral_angle_3_deg 16.291 r_dihedral_angle_4_deg 13.252 r_dihedral_angle_1_deg 9.018 r_angle_refined_deg 1.442 r_angle_other_deg 1.048 r_chiral_restr 0.08 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.091 r_dihedral_angle_3_deg 16.291 r_dihedral_angle_4_deg 13.252 r_dihedral_angle_1_deg 9.018 r_angle_refined_deg 1.442 r_angle_other_deg 1.048 r_chiral_restr 0.08 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 874 Nucleic Acid Atoms Solvent Atoms 6 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing PDB_EXTRACT data extraction